Natural populations have a large amount of genetic variation at the DNA level. How much and why such genetic variation is maintained in a population is one of the most important questions in population genetics. In this research project, I have worked on this subject and obtained the following results.In order to understand the mechanism of maintenance of DNA polymorphism, we have to measure the amount of DNA polymorphism accurately. There are several statistical methods for estimating the amount of DNA polymorphism. Many of them, however, cannot be used when selective constraints are different among different sites. In this research project, I have developed a new statistical methods for estimating the amount of DNA polymorphism, which can be used even when selective constraints are different among different sites. I have also obtained a new statistical methods for estimating the amount of DNA polymorphism from AFLP data.When a natural selection is operating on a particular site, we cannot use the neutral theory. I have works on the effect of natural selection on the amount and pattern of DNA polymorphism. One of interesting results is that even when a natural selection is operating on a particular site, we can still estimate the amount of DNA polymorphism in terms of 4Nv, where N is the effective population size and v is the mutation rate. Furthermore, we can estimate the ancestral DNA sequence of the DNA sequences sampled from a population. I have also studied the effect of population structure on the amount of DNA polymorphism.DNA多型の量は部位ごとに中立突然変異率が異なっているため、従来の方法で推定すると過小評価してしまう。この過小評価を補正する式を開発した。また、最近開発された方法、すなわちAFLP法、で得られたデータを解析する統計的方法を開発した。分集団化や移住はDNA多型の量やパターンを決定する重要な要因である。分集団化した2集団がその後しばらく移住の影響を受けるというモデルの下で、DNA多型の量やパターンをみると、その影響は、集団の大きさや移住率だけでなく、移住が行われている期間の重要であることが明らかになった。